The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota
Open accessAbstract
SUMMARY: The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease.
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The formation of intestinal microbiota during childhood is a key factor in the development of human diseases, such as allergies, neurological disorders and obesity.
“The formation of intestinal microbiota during childhood is believed to be a key factor in the development of human diseases, such as allergies, neurological disorders and obesity (2–4)”
From Kefir and Intestinal Microbiota Modulation: Implications in Human Health (2021) · cites this paper as [3]
The Allergy section (p. 31) links infant gut microbiota development to later allergic disease, and Metabolic Disorders (p. 33) says factors affecting its establishment may contribute to later obesity risk. Our copy does not link childhood microbiota formation to neurological disorders; its mention of brain developmental programming (p. 33) concerns obesity. (LLM, conf=0.86)
Experimental — accuracy not yet measuredDysbiosis and other determinants of intestinal microbiota formation in childhood, such as birth via cesarean section or formula feeding, are associated with a higher risk of developing obesity, both in child and adulthood.
“Dysbiosis and other determinants of intestinal microbiota formation in childhood, such as birth via cesarean section or formula feeding, are associated with a higher risk of developing obesity, both in child and adulthood (3, 68).”
From Kefir and Intestinal Microbiota Modulation: Implications in Human Health (2021) · cites this paper as [3]
The Metabolic Disorders section (p. 33) links early-life microbiota disturbances, nutrition, and delivery mode with later obesity; the discussion of delivery mode (p. 11) specifically associates cesarean birth with higher obesity incidence. It also reports obesity in children and adults in connection with early antibiotic exposure (p. 33). The passages found do not specifically link formula feeding to increased obesity risk, so that example is not supported by this source. (LLM, conf=0.86)
Experimental — accuracy not yet measuredThe development of diabetes mellitus is associated with low-grade chronic inflammation.
“The development of diabetes mellitus is associated with low-grade chronic inflammation.”
From Kefir and Intestinal Microbiota Modulation: Implications in Human Health (2021) · cites this paper as [3]
The section “Other Long-Lasting Effects of the Infant Gut Microbiota” (p. 34) says that early microbiota perturbations may create a proinflammatory environment that facilitates autoimmune disease, in its discussion of type 1 diabetes. It does not characterize this as low-grade chronic inflammation or extend the association to diabetes mellitus generally. (LLM, conf=0.82)
Experimental — accuracy not yet measuredChanges in intestinal permeability, favored by an imbalance in the intestinal microbiota, encourage low-grade chronic inflammation, leading to systemic insulin resistance and diabetes.
“Changes in intestinal permeability, which are favored by an imbalance in the intestinal microbiota, encourage the occurrence of this inflammation, which leads to resistance to systemic insulin, with consequent development of diabetes (3, 75).”
From Kefir and Intestinal Microbiota Modulation: Implications in Human Health (2021) · cites this paper as [3]
The Metabolic Disorders section (p. 33) links intestinal-barrier function and early-life microbiota disruption to metabolic health, and reports insulin resistance and type 2 diabetes after microbiota alteration in mouse studies. The Other Long-Lasting Effects section (p. 34) says infant microbiota perturbations may create a proinflammatory environment relevant to type 1 diabetes. Neither passage establishes the claimed sequence in which dysbiosis increases intestinal permeability, causing chronic inflammation that leads to systemic insulin resistance and diabetes; the paper also cautions that a causal link in humans remains to be established. (LLM, conf=0.86)
Experimental — accuracy not yet measuredFactors affecting the formation of intestinal microbiota, such as maternal health during pregnancy, birth via cesarean section, use of antibiotics during childhood, and intestinal dysbiosis in childhood, are related to the development of diabetes.
“In addition, factors that affect the formation of the intestinal microbiota—such as maternal health during pregnancy, birth via cesarean section, the use of antibiotics during childhood, and the presence of intestinal dysbiosis in childhood—are also related to the development of diabetes (3).”
From Kefir and Intestinal Microbiota Modulation: Implications in Human Health (2021) · cites this paper as [3]
Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measured
The correct formation of intestinal microbiota during childhood is fundamental for the complete development of the baby because the intestinal microbiota is part of the immune system, especially in the first months of life.
“The correct formation of intestinal microbiota during childhood is fundamental for the complete development of the baby, since the intestinal microbiota is part of the immune system, being important especially in the first months of life, when the rest of the immune system is still forming.”
From Kefir and Intestinal Microbiota Modulation: Implications in Human Health (2021) · cites this paper as [3]
The Infant Intestinal Colonization Process: the Foundation of Health (p. 29) says early microbiota is necessary for adequate maturation of the gut and associated immune system and is critical for host maturation. Impact of Early-Life Microbiota on Long-Lasting Physiological Effects (p. 31) emphasizes microbial interactions in the earliest days of life. The paper describes the microbiota as influencing immune development, not as itself part of the immune system. (LLM, conf=0.84)
Experimental — accuracy not yet measuredPremature babies may have immaturity in the immune, respiratory and neurological systems, suggesting a possible relationship between them.
“In this context, premature babies may have immaturity in the immune, respiratory and neurological systems, suggesting a possible relationship between them (3).”
From Kefir and Intestinal Microbiota Modulation: Implications in Human Health (2021) · cites this paper as [3]
The ‘Gestational age at birth’ passage (p. 11) says preterm infants often have an immature gut and immune, respiratory, and neurological issues. It does not suggest a relationship among the immune, respiratory, and neurological systems, so that part of the claim is unsupported. (LLM, conf=0.85)
Experimental — accuracy not yet measuredEarly life factors may still have long-lasting implications for the physical and mental health of the individual.
“these early life factors may still have long-lasting implications for the physical and mental health of the individual (Callaghan et al., 2019;Gensollen et al., 2016;Milani et al., 2017), consistent with the idea that there are sensitive periods for microbiota-gut-brain interactions.”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Milani et al., 2017
The section “Impact of Early-Life Microbiota on Long-Lasting Physiological Effects” (p. 31) says early-life microbial disruption may have lasting physiological and immune consequences; “Metabolic Disorders” (p. 33) discusses later metabolic health. These passages support the physical-health part of the claim, but the copy does not establish a long-lasting effect on mental health. The paper also addresses early-life factors insofar as they affect gut microbiota, rather than early-life factors generally. (LLM, conf=0.84)
Experimental — accuracy not yet measuredMicroorganisms are not necessarily negative or the cause of diseases; they co-evolved with human hosts and their presence can be important for maintaining health.
“On the contrary, it is increasingly clear that they co-evolved with human hosts and the presence of microorganisms can be important for maintaining health (1–4).”
From Kefir and Intestinal Microbiota Modulation: Implications in Human Health (2021) · cites this paper as [3]
Children treated with antibiotics, specially macrolides, amoxicillin, cefdinir, vancomycin, and tetracyclines, had a higher incidence of obesity, since antibiotics can alter the composition of the intestinal microbiota, leading to a dysbiotic state.
“Children treated with antibiotics, specially macrolides, amoxicillin, cefdinir, vancomycin, and tetracyclines (69) had a higher incidence of obesity (3), since antibiotics can alter the composition of the intestinal microbiota, leading to a dysbiotic state (3, 70).”
From Kefir and Intestinal Microbiota Modulation: Implications in Human Health (2021) · cites this paper as [3]
Individuals with autism have a characteristic intestinal microbiota, which strengthens the relationship between intestinal microbiota and neurological disorders.
“In addition, individuals with autism have a characteristic intestinal microbiota, which strengthens the relationship between intestinal microbiota and neurological disorders (1–4).”
From Kefir and Intestinal Microbiota Modulation: Implications in Human Health (2021) · cites this paper as [3]
The discussion of long-lasting effects (p. 34) addresses IBD, IBS, and type 1 diabetes, but not autism. Searches of our copy for autism and neurological disorders found no passage describing a characteristic intestinal microbiota in autistic individuals or linking that finding to neurological disorders. (LLM, conf=0.74)
Experimental — accuracy not yet measuredBreast-fed infants have consistently greater levels of bifidobacteria and an overall lower diversity compared to formula-fed infants.
“breast-fed infants have consistently greater levels of bifidobacteria and an overall lower diversity compared to formula-fed infants (Milani et al., 2017).”
From Viral Infections, the Microbiome, and Probiotics (2021) · cites this paper as Milani et al., 2017
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“Compared to formula-fed infants, breastfed infants have been shown to possess higher levels of bifidobacteria and lacto-bacilli [11], along with a lower abundance of the Bacteroides genus and potential pathogens belonging to clostridia, enterobacteria, enterococci and staphylococci [1].”
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The road not taken: host genetics in shaping intergenerational microbiomes
Zeng, S., Wang, S., Ross, R. P., & Stanton, C. (2022) · Trends in Genetics · doi:10.1016/j.tig.2022.05.016 · Cited by 9 · see citing works
The role of teichoic acids of bifidobacteria in driving the interaction with the human host
Longhi, G., Vergna, L. M., Lugli, G. A., Bianchi, M. G., Tarracchini, C., Milani, C., Turroni, F., Bussolati, O., van Sinderen, D., & Ventura, M. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1616397 · Cited by 6 · see citing works
Self-citationFreitas, A. C., Li, G., Shawon, J., Qamar, H., Pell, L. G., Kabir, M., Oduaran, O. H., Puebla-Barragan, S., Bassani, D. G., O'Callaghan, K. M., et al. (2025) · mSphere · doi:10.1128/msphere.00314-25 · Cited by 6 · see citing works
- Authors
- Milani, C., Duranti, S., Bottacini, F., Casey, E., Turroni, F., Mahony, J., Belzer, C., Delgado Palacio, S., Arboleya Montes, S., Mancabelli, L., Lugli, G. A., Rodriguez, J. M., Bode, L., de Vos, W., Gueimonde, M., Margolles, A., van Sinderen, D., & Ventura, M.
- Affiliations
- University of Parma (IT)
- National University of Ireland (IE)
- Wageningen University & Research (NL)
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
- Department of Nutrition, Food Science and Food Technology, Complutense University of Madrid, Madrid, Spain
- University of California San Diego (US)
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Consejo Superior de Investigaciones Científicas (ES)
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
- ORCID
- Venue
- Microbiology and Molecular Biology Reviews
- Publisher
- American Society for Microbiology
- Published
- 2017-12
- Volume
- 81
- Issue
- 4
- ISSN
- 1092-2172 (ISSN-L)
- 1098-5557
- PMC
- PMC5706746
- OpenAlex
- W2767360135
- Semantic Scholar
- 632e13fa6d1709c03f031492eea621c2167514f5
- Cited by
- 1,950
- References
- 552
- Citations by year
- 2026: 165 · 2025: 247 · 2024: 285 · 2023: 268 · 2022: 288 · 2021: 290 · 2020: 246 · 2019: 107 · 2018: 47 · 2017: 4
- FWCI
- 10.41
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Microbiology and Molecular Biology Reviews (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Socio-Environmental Systems Modeling (acceptedVersion)
- Arrow@dit (Dublin Institute of Technology) (submittedVersion)
- Cork Open Research Archive (University College Cork, Ireland) (submittedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Funders
- Science Foundation Ireland (SFI/12/RC/2273, 15/SIRG/3430)
- Ministero dell'Istruzione, dell'Università e della Ricerca
- Ministerio de Economía y Competitividad (PCIN-2015-233, AGL2016-75476-R)
- Danone
- EU Joint Programming Initiative “A Healthy Diet for a Healthy Life”
- Spanish Plan Estatal de I+D+I (AGL2016-78311-R)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Keywords
- infant gut microbiota, neonatal gut colonization, breast milk, Bifidobacterium, host-microbe coevolution, asthma, inflammatory bowel disease, metabolic disorders, functional foods, microbiota modulation
- MeSH terms
- Infant Health, Gastrointestinal Microbiome, Whole Genome Sequencing, Breast Feeding, Female, Humans, Immune System, Infant, Intestinal Diseases, Maternal-Fetal Exchange, Milk, Human, Pregnancy, Symbiosis, Biomarkers, Probiotics, Gastrointestinal Tract
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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